Kuratani Mitsuo, Yoshikawa Yuka, Bessho Yoshitaka, Higashijima Kyoko, Ishii Takeshi, Shibata Rie, Takahashi Seizo, Yutani Katsuhide, Yokoyama Shigeyuki
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Structure. 2007 Dec;15(12):1642-53. doi: 10.1016/j.str.2007.09.020.
In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.
在细菌遗传密码系统中，密码子AUA由位于摆动位置带有赖氨酸残基的tRNA（Ile）（2）解码为异亮氨酸。赖氨酸残基由胞苷通过tRNA（Ile）赖氨酸合成酶（TilS）与ATP和L-赖氨酸生成，TilS是一种N型ATP焦磷酸酶。在本研究中，我们确定了嗜热栖热菌TilS与ATP、Mg2+和L-赖氨酸形成复合物的晶体结构，分辨率为2.5埃。TilS特异性亚结构域的存在导致活性位点有两个独立的通道，一侧是一个大洞，另一侧是一条狭窄的隧道。ATP结合在洞内，L-赖氨酸结合在隧道入口处。PP模体中保守的Asp36与Mg2+配位。在这些初始结合模式中，ATP、Mg2+和L-赖氨酸彼此相距很远，但在胞苷结合时，它们似乎会聚集在一起发生反应，复合物可能会发生结构变化。
